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Conserved domains on  [gi|2567559086|ref|WP_306461466|]
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exodeoxyribonuclease V subunit gamma, partial [Colwellia ponticola]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecC super family cl39130
Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 1-137 3.61e-48

Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1330:

Pssm-ID: 440941 [Multi-domain]  Cd Length: 1087  Bit Score: 165.01  E-value: 3.61e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLgrDE 79
Cdd:COG1330     10 LEVLADLLAALLAAQPLAdPFAPEVILVQSPGMARWLQLELAER--------FGIAANIEFPLPASFIWQLFRAVL--PD 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:COG1330     80 VPEESPFSKEALTWRLMRLLPELLDEPEFAPLARYLGDDEDQRKRYQLAGRLADLFDQ 137
 
Name Accession Description Interval E-value
RecC COG1330
Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 1-137 3.61e-48

Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440941 [Multi-domain]  Cd Length: 1087  Bit Score: 165.01  E-value: 3.61e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLgrDE 79
Cdd:COG1330     10 LEVLADLLAALLAAQPLAdPFAPEVILVQSPGMARWLQLELAER--------FGIAANIEFPLPASFIWQLFRAVL--PD 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:COG1330     80 VPEESPFSKEALTWRLMRLLPELLDEPEFAPLARYLGDDEDQRKRYQLAGRLADLFDQ 137
recC TIGR01450
exodeoxyribonuclease V, gamma subunit; This model describes the gamma subunit of ...
 1-137 1.36e-45

exodeoxyribonuclease V, gamma subunit; This model describes the gamma subunit of exodeoxyribonuclease V. Species containing this protein should also have the alpha (TIGR01447) and beta (TIGR00609) subunits. Candidates from Borrelia and from the Chlamydias differ dramatically and score between trusted and noise cutoffs. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273633 [Multi-domain]  Cd Length: 1060  Bit Score: 157.98  E-value: 1.36e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDPedddmggcGIAAAIDVQLPGSFMWQLYRMVLGrdE 79
Cdd:TIGR01450    9 LDVLAALLAALLRDPPLDdPFEPELILVQSPGMAQWLQMTLAEDL--------GVAANLEFPLPASFIWQMFVAVLP--E 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:TIGR01450   79 IPEESAFNKEVMSWRLMALLPALLERPEFRTLRHYLADDSDLRKRYQLAERLADLFDQ 136
Exonuc_V_gamma pfam04257
Exodeoxyribonuclease V, gamma subunit; The Exodeoxyribonuclease V enzyme is a multi-subunit ...
 1-137 1.92e-44

Exodeoxyribonuclease V, gamma subunit; The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA. This subunit recognizes and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilize the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair.


Pssm-ID: 461240 [Multi-domain]  Cd Length: 308  Bit Score: 147.08  E-value: 1.92e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086   1 MDELRSLVVSWMRRYPLAPLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLGRDei 80
Cdd:pfam04257   9 LEVLAELLAALLRRPLADPFEPEIILVQSKGMARWLTLELAEK--------FGIAANIEFPFPASFLWKLFRAVLGKL-- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2567559086  81 PPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:pfam04257  79 PEESPFAKEVLTWRLMRLLPELLEQPEFAPLRHYLADDGDQLKLFQLAERIADLFDQ 135
recC PRK11069
exodeoxyribonuclease V subunit gamma;
1-137 5.72e-41

exodeoxyribonuclease V subunit gamma;


Pssm-ID: 236835 [Multi-domain]  Cd Length: 1122  Bit Score: 144.69  E-value: 5.72e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLgrDE 79
Cdd:PRK11069    10 LDVLKALMVFLIEREPLDdPFEPEMILVQSPGMAQWLQMELAQK--------FGIAANIDFPLPATFIWDMFTRVL--PD 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:PRK11069    80 IPKESAFNKEAMTWKLMTLLPQLLERPEFTPLRHYLTDDEDKRKLFQLAARIADLFDQ 137
 
Name Accession Description Interval E-value
RecC COG1330
Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 1-137 3.61e-48

Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440941 [Multi-domain]  Cd Length: 1087  Bit Score: 165.01  E-value: 3.61e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLgrDE 79
Cdd:COG1330     10 LEVLADLLAALLAAQPLAdPFAPEVILVQSPGMARWLQLELAER--------FGIAANIEFPLPASFIWQLFRAVL--PD 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:COG1330     80 VPEESPFSKEALTWRLMRLLPELLDEPEFAPLARYLGDDEDQRKRYQLAGRLADLFDQ 137
recC TIGR01450
exodeoxyribonuclease V, gamma subunit; This model describes the gamma subunit of ...
 1-137 1.36e-45

exodeoxyribonuclease V, gamma subunit; This model describes the gamma subunit of exodeoxyribonuclease V. Species containing this protein should also have the alpha (TIGR01447) and beta (TIGR00609) subunits. Candidates from Borrelia and from the Chlamydias differ dramatically and score between trusted and noise cutoffs. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273633 [Multi-domain]  Cd Length: 1060  Bit Score: 157.98  E-value: 1.36e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDPedddmggcGIAAAIDVQLPGSFMWQLYRMVLGrdE 79
Cdd:TIGR01450    9 LDVLAALLAALLRDPPLDdPFEPELILVQSPGMAQWLQMTLAEDL--------GVAANLEFPLPASFIWQMFVAVLP--E 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:TIGR01450   79 IPEESAFNKEVMSWRLMALLPALLERPEFRTLRHYLADDSDLRKRYQLAERLADLFDQ 136
Exonuc_V_gamma pfam04257
Exodeoxyribonuclease V, gamma subunit; The Exodeoxyribonuclease V enzyme is a multi-subunit ...
 1-137 1.92e-44

Exodeoxyribonuclease V, gamma subunit; The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA. This subunit recognizes and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilize the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair.


Pssm-ID: 461240 [Multi-domain]  Cd Length: 308  Bit Score: 147.08  E-value: 1.92e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086   1 MDELRSLVVSWMRRYPLAPLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLGRDei 80
Cdd:pfam04257   9 LEVLAELLAALLRRPLADPFEPEIILVQSKGMARWLTLELAEK--------FGIAANIEFPFPASFLWKLFRAVLGKL-- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2567559086  81 PPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:pfam04257  79 PEESPFAKEVLTWRLMRLLPELLEQPEFAPLRHYLADDGDQLKLFQLAERIADLFDQ 135
recC PRK11069
exodeoxyribonuclease V subunit gamma;
1-137 5.72e-41

exodeoxyribonuclease V subunit gamma;


Pssm-ID: 236835 [Multi-domain]  Cd Length: 1122  Bit Score: 144.69  E-value: 5.72e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2567559086    1 MDELRSLVVSWMRRYPLA-PLENEIALVQSNGIAQWLKLALAEDpedddmggCGIAAAIDVQLPGSFMWQLYRMVLgrDE 79
Cdd:PRK11069    10 LDVLKALMVFLIEREPLDdPFEPEMILVQSPGMAQWLQMELAQK--------FGIAANIDFPLPATFIWDMFTRVL--PD 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2567559086   80 IPPKSLLDKAPLTWRLMRLLPELIDQQHFEPLQRFLTHDSDLRKRYQLAERLADLFDQ 137
Cdd:PRK11069    80 IPKESAFNKEAMTWKLMTLLPQLLERPEFTPLRHYLTDDEDKRKLFQLAARIADLFDQ 137
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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